Contacts of the helix formed by residues 614 - 623 (chain D) in PDB entry 1S77
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 614 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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585D ASP 2.9 18.8 - - - +
586D ALA* 2.8 24.6 - - - +
587D ILE 4.1 12.4 + - - +
588D ASN* 4.6 1.1 - - - +
589D GLY 3.2 15.5 + - - +
590D THR* 3.3 23.3 + - - +
591D ASP* 4.4 15.4 + - + +
613D THR* 1.3 87.8 - - - +
615D ALA* 1.3 55.5 + - + +
616D LEU 3.1 1.5 - - - +
617D ALA* 3.7 3.7 - - - +
618D GLY* 2.8 30.7 + - - -
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Residues in contact with ALA 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592D ASN* 3.6 32.5 - - - +
611D LEU* 4.7 7.4 - - + -
612D GLY 4.3 1.3 - - - +
613D THR 2.4 8.8 + - - +
614D LYS* 1.3 78.5 - - + +
616D LEU* 1.3 59.5 + - - +
618D GLY* 3.7 1.4 + - - -
619D GLN* 3.3 29.9 + - - +
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Residues in contact with LEU 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D LEU* 3.6 44.9 - - + +
612D GLY 3.0 19.9 + - - +
613D THR* 3.9 6.7 - - - +
615D ALA* 1.3 78.5 - - - +
617D ALA* 1.3 63.4 + - - +
619D GLN* 3.3 27.1 - - - +
620D TRP* 3.4 14.0 - - - -
672D GLN* 3.8 14.8 - - + +
673D ALA* 4.2 15.0 - - + +
676D TYR* 3.4 42.6 - - + -
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Residues in contact with ALA 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LEU* 3.5 38.5 - - + +
585D ASP* 3.9 9.2 - - + -
586D ALA 4.2 2.5 - - - +
614D LYS 3.3 10.0 + - - +
616D LEU* 1.3 77.3 - - - +
618D GLY* 1.3 55.1 + - - +
620D TRP* 3.0 4.2 + - - +
621D LEU* 2.7 39.4 + - - +
676D TYR* 3.2 22.3 - - - +
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Residues in contact with GLY 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586D ALA* 5.5 1.8 - - - -
614D LYS 2.8 20.3 + - - -
615D ALA* 4.1 2.5 - - - -
617D ALA* 1.3 72.2 - - - +
619D GLN* 1.3 51.5 + - - +
621D LEU* 2.9 16.2 + - - +
622D ALA* 2.5 37.3 + - - +
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Residues in contact with GLN 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D LEU* 3.1 31.8 - - - +
615D ALA* 3.3 19.4 + - - +
616D LEU* 3.3 22.2 - - - +
618D GLY* 1.3 74.7 - - - +
620D TRP* 1.3 58.0 + - + +
622D ALA* 3.0 10.9 + - - +
623D TYR* 2.8 25.5 + - - +
666D MET* 3.3 28.5 - - + +
667D PHE* 3.5 30.5 - - + +
668D THR* 3.6 8.8 + - - +
673D ALA* 4.4 2.4 - - - +
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Residues in contact with TRP 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LEU* 3.8 16.8 - - + -
616D LEU 3.4 20.3 + - - -
617D ALA 3.0 7.0 + - - +
619D GLN* 1.3 78.1 - - + +
621D LEU* 1.3 66.3 + - - +
623D TYR* 3.0 31.9 + + + +
624D GLY 3.3 6.4 + - - -
625D VAL* 3.6 18.9 + - + +
629D VAL* 4.1 14.1 - - + -
650D VAL* 3.5 22.0 - - + -
654D THR* 4.2 3.6 - - - -
655D ILE* 3.4 28.3 - - + -
667D PHE* 3.8 21.5 - + - -
673D ALA* 2.7 39.1 + - - +
676D TYR* 3.6 19.6 - + - -
677D MET* 3.2 31.6 - - + +
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Residues in contact with LEU 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D ASN* 4.6 9.4 - - - +
582D LEU* 3.8 31.9 - - + +
583D GLN* 3.9 23.8 - - + +
586D ALA* 3.7 31.0 - - + -
617D ALA 2.7 25.4 + - - +
618D GLY* 3.2 11.4 - - - +
620D TRP* 1.3 69.6 - - - +
622D ALA* 1.3 66.7 + - - +
623D TYR 3.7 5.2 - - - +
624D GLY* 4.3 2.3 + - - -
625D VAL* 5.6 0.4 - - - -
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Residues in contact with ALA 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D GLY 2.5 16.1 + - - +
619D GLN* 3.0 16.6 + - - +
621D LEU* 1.3 71.8 - - - +
623D TYR* 1.3 67.8 + - - +
666D MET* 3.9 19.6 - - + +
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Residues in contact with TYR 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D GLN 2.8 9.1 + - - +
620D TRP* 3.0 28.9 + + + +
621D LEU 3.7 3.0 - - - +
622D ALA* 1.3 89.4 - - - +
624D GLY* 1.3 76.8 + - - +
625D VAL* 3.8 7.2 - - - -
626D THR* 6.0 0.7 - - - -
629D VAL* 4.5 17.3 - - + -
654D THR* 3.7 22.4 + - - -
658D ALA* 3.7 24.8 - - + +
663D LYS* 4.2 9.6 - - + -
666D MET* 3.2 29.3 - - + +
667D PHE* 3.6 22.0 - + + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il